I've dealt with CRLF problems before, but what kind of control characters are these (if that's what they are), and why is it that I could only find them using the perl debugger?

You have encountered CRLF in one of their many disguises. \cM is ^M is <CR>, and \cJ is ^J is <LF>.

As to why you're not seeing them in your editor, I dunno. Does your editor have a setting for showing control characters?